CHEM BIO 2 Flashcards
How does bacterial transcription differ from eukaryotic
bacteria is done next to ribosome translated
immediately,
bacterial 5’end is a triphosphate
eukaryotic - done in nucleus and transported out ,
2) it has introns to be removed or kept in,
3) has 5’ capping and
4) has poly a tail post transcriptionally
Why do we splice mRNA
biodiverstiy
What and why do we have a 5’ g cap
It is literally GTP applied to the 5 end - Protects the end, disguises it as a 3’ end , prevents degradation and is a (ESSENTIAL FOR LOADING) binding site for ribosome
Why do we have poly A tail
direct mRNA to ribosome - - comes from a POLY A polymerase binder - 50-200 A’s
Know RNA processing steps
draw it out - pol II binds , as soon as transcribed - cap installation - then splicing occurs at splice site - once released - poly A tail from polyemrase - then exported to ribosome - cap and poly a tail have protein protein interactions - then DECAP - marks it for degradation
What does ribonuclease H do
- removes RNA primers from DNA replications - recognizes RNA-DNA hybrid and cuts out RNA - high specificity - good in lab(eg if mRNA pathogenic - can bind antisense DNA and cut it out
Can phosphates be chiral
yeah
What reaction does the ribosom ecatalyze
aminolysis of alpha amino esters (SIMPLE KNOW HOW TO DRAW)
What catalyzes the aminolysis of alpha amin esters
Lone pair on N3 of adenine deprotonates amino group (pKa ~7.6, over 10,000x more basic than N3 of free A due to H-bonding
)
What is energy used for in protein synth
In moving them along the protein and fideltiy
Are amino acids checked?Relevance?
NOPE only based on codon anti codon - SO if can generate an amino acid with the right codon ou can stick whatever you want on there to be added
What is tRNA synthase responsible for
f9idletiy of translation - couplesATP to amino acylation and 2 active site can have different specificity - this ATP attachment is largely done by attaching AMP to something - it’s a good leaving group
Using ATP for an nufvaroable reaction - particular joining amino acid to trna
so ATP binds to amino acid but the pyrophosphate cleaves off - has AMP as a good leaving group so tRNA can attach 9know how to draw - tRNA synthase slide - in notes)
What is a riboswitch
regions on the nascent 3’ RNA THAT CAN BIND SMALL MOLECULES THAT AFFECT translationg - 2 important regions are the termination sequence and aptarmer site which is a ligand binding site - - can cause conformation changes to terminate transcription
t
are peptide sequences directional?
yeah
PRACTICE TELLING IS AN AMINO ACID IS CHARGED OR NOT GIVEN ITS PKA
Most important force for protein folding and name 3 examples
Non polar interactions such as arene-arene, cation pi, dispersive, much more common than H bonds and salt bridges
What are most often the conserved parts of protein structure
hydrophobic core
What are the general forces that control protein secondary and tertiary structure
H-bonds
Dipoles
Sterics
Hydrophobic effect
BUT sterics and dipoles real important
Go over the sterics/ and A12 vs A3 strain again
Know how to draw it - so the A13 comes from the phi bond on the next main oacid and A12 comes from the not phi strain of the same amino acid (can tell byh counting bonds A13 should have 4 bonds total, A12 3) and A13 is the one that is really defining the energy and shape of peptide
Go over the sterics/ and A12 vs A3 strain again
in notes
What is the arrangement for alpha helix in terms of h bonding and why (what are other possible(
i + 4 - most stable (h bond angle matters) i+3 makes a 3:10 helix and i + 2 makes a serpentine shape - gamma turn s- not often used
Alpha helix macrodipoles - describe them
From the N to C terminal have + to negative general macrodipole
amino acids with issues with alpha helix
Proline, glycine and beta branched hydrophobics
What are the turns you can make and what do they depend on (peptide chains)
Beta (180 degree turn) and gamma turn (90 degree) - beta is an I and i+3 H bond whereas gamma is an I and I+2 h bond
where are majro structures on ramachandran plot
see notes
cysteine vs cystine (which direction redox)
unbonded vs disufide bridge -reducing seperates them oxidative conditions bind them
Some basic protein motifs
Leucine zipper and zinc finger bind DNA, beta sandwiches are common architecture, collagen triple left handed helix, 7 TM and beta barrel span membranes
Beta branched amino acids means what for structure?
Bad for alpha helices good for beta sheets
What aere our two activation energies in our energy plot for an enzyme
There’s Ea from initial to largest peak - and this is km/cat - this is assuming [S] is limited BUT if [s] is saturated we have Ea kcat - which is just based on enzyme turnover (from 1sts stable state to second peak
either can be the slow step
Wht is km mathematically
kcat + k-1 / k1 (can think of as things moving away from ES divided by constant moving towards Es
Why do we use Kcat/km
for enzyme efficiency - use this because Km can vary so much by various terms hard to just pin point what is making km small
What is kcat/km
Slope of our [s] vs ks plot - 2nd order constant
If we add an inhibitor that effects E (instead of E +S we get E+I lowers its initial energy) what are the changes and how does that change our various plots (energy diagram, [s] plot)
so it will increase our activation energy (the initial condition is at a lower energy - BUT note it only changes our first Ea (ea kcat/km?) I guess as opposed to just Ea Kcat because the the stable intermediate to the transition state of forming the product is in the same place so that ea doesn’t change. ON our [s] plot - it changes the initial slop because that’s kcat/km and km is increasing now -
What are the phi and trident angles
phi is between N and R and trident is between O and R- Phi is A12 hinderance and trident is A13 hinderance (bigger - A13 is 2 apart and a12 is 1 apart)
Phi and trident angles for common motifs
-90, 150 for Beta pleated and -90, -60 for alpha helices
What is kd mathematically
Koff / Kon
Are alpha helices stabilized by h bonds between backbone amides int he same hellix? true or false
True
Are glycines commonly found in alpha helices?
No, because glycine so flexible can break helices
Are the amino acid side chains in a beta sheet all facing the same direction
No
Are beta sheets held together by h bonds between back bone amides in different strands?
Yes
Native peptide ligation requires what on the N terminus
a Cystine
What are the beta branched amino acids
Valine isoleucine threonine
what makes a leucine zippe
a leuceine every 7 amino acids
2 key assumptions for michaelis menten
1) product formation concentration is so low it’s negligible and the product binding to enzyme is negligible/non existent and 2) formation and breakdown of ES is equivalent such that ES is constant
What are the axes on a lineweaver burke plot
1/[s] and 1/vo
On a line weaver burke plot where are the key points
The x intercept is -1/km with competitiv inhibition km increases so this point gets closer to 0, The y intercept is -1/Vm - so when we get uncompetitive inhibition this changes
Uncompetitive inhibitor snad non (mixed) competitive inhibitors effect on Km and vmax
uncompetitive inhibitors decrease Vmax AND km, while mixed decrease Vmax and sometimes Km
Whats the equation for competitive inhibition
V = Vmax [S] / (Km(1+[I]/Ki) + [S])
What do the followig co factors do:
Folate
S-adenylmethionine
Nicotinamide Adenine Dinucleotide
Pyridoxal Phosphate
Biotin
Thymine Pyrophosphate
Folta carries one carbon units (methyl, formyl, methylene to transfer to other molecules)
S-adenylmethionine - transfers one carbon as methyl and provides for enzymes as a donor)
NAD NADH - redox reactions
Pyridoxal Phosphate - catalyzes reactions for racemization, decarboxylation and deamination of amino acids
Biotin - transports carboxylate groups between active sites
Thymine Pyrophosphate - thiazolium carbon nucleophile can attack carbonyls, stabilizes carbanions for biosynth orcatabolic reactions
Delta G from energy plot
Efwd - e rev (which is startig state to apex)
Other consdierations in rate experiments
How much of enzyme actually active (does []= [] of active enzyme) and also want substrate way bigger than enzyme amount such that the amount of substrate lost is negligible (so don’t need to factor in “free remaining R” should be very similar to initial cncentration
What is the equation for v
]vmax*[s] / (km + [s] (so this way when [s] = km v is 1/2 vmax
kcat vs kcat/km for rate constants
kcat is 1st order rate oconstant at saturated [s], whereas kcat/km is the 2nd order rate constant for free enzyme and free s
does tyrosine have a pka?
yeah
what does coenzyme A do
acyl group carrier
NAD+ /NADPH
Are dissociations unimolecular
you bet
T/F for pH sensitive in terms of binding
I guess can just say yes i fknown histidine
Both parallel and anit parallel beta plested sheets are stabilized through h bonds of backbone amides from 2 or more beta sheets (T/fF)
true
peptide vs invivo systnheises
peptide is C to N (as in new amino acids are their C to the existing N); in vivo its N to C in which amino acids add their N to the existing C
Zn 2+ in catalytic site
Acts as lewis acid - can active carbonyl for attack
test for Kd experiment for competitive binding
AN equillibiurm binding assay - compare concentraiton bound figure out Kd in presence of and wihtout inhibitor
How does PLP work
aldehyde - forsm imine with amino acid - conjugated bond system - acitvates bond next to imine
Mechanism based vs transition state inhibitor
mechanism based more ikely to interact with functional groups in active site - make covalent bonds - both bind in active site tho
FOr a small molecule which is more important k off or k on
k off
What is Vmax
The rate under saturated substrate
uncompetitive vs non competitive
Non-competitive inhibitors bind equally well to the enzyme and enzyme–substrate complex. Uncompetitive inhibitors bind only to the enzyme–substrate complex - uncompetitive lower both kcat AND km (kcat/km stays the same) non competitive inhibitors decrease Kcat and don’t effect Km so kcat/km goes down
All the inhibition types and effects on graphs
Competitive - increase Km - kcat the same (so for lineweaver burke - more inhibited means smaller x intercept - y intercept the same)
uncompetitive - Decreases Km AND kcat - So as we increase inhibition x intercept actually gets bigger AND our y intercept gets bigger
Non competitive - decreases Kcat keeps Km the same - so should all have same x intercept but y intercept gets bigger with more inhibition
Mixed competitive - Km can get bigger vmax can get bigger - so with more Inhibition x intercept gets smaller (km bigger) and vmax smaller (y intercept bigger)
NAD+ vs NADP
NAD+ for catabillic, NADPH for analbolic
